I know this is an old thread, but we never heard back on this.
The fuel is pulled from the tank to the pump, first via the the bowl. The connection on the banjo fitting (on top of the bowl) can suck air and you won't know it. Those washers that seal the banjo (and all banjos on the fuel system) have a rubber seal made into them. If that seal is crushed enough, it will not seal and allow air into the system.
Also, start at the most simplest parts first. Sometimes a new fuel filter will fail. They get clogged with fungus and blocks flow. Not very common, but common enough. Use and anti-fungal additive if you live in those areas where those conditions are prevalent.
(1) Pump fuel system by hand until pressure is built up.
(2) Loosen connection on injection pump and see if flow is good. If not follow that line backwards until you find the culprit.
(3) If you have good flow to the injection pump, then it could be the pump or the lines obstructed or the injectors are clogged/damaged.